Citrus sinensis cv. Neixiu genome v1.0

Overview


Analysis Name	Citrus sinensis cv. Neixiu genome v1.0
Method	Illumina Novaseq 6000, PacBio Sequel II, Hi-C (Assembled with SOAP v2.21, Hifiasm v0.16, LACHESIS)
Source	GCA_038048705.1
Date performed	2024-05-30

About the assembly

For this genome, please cite Yang L, Deng H, Wang M, Li S, Wang W, Yang H, Pang C, Zhong Q, Sun Y, Hong L. A high-quality chromosome-scale genome assembly of blood orange, an important pigmented sweet orange variety. Scientific data. 2024 May 06; 11(1):460. The assembly was originally downloaded from NCBI and the annotation from Figshare.

Assembly metrics

Assembly size	335 Mb
Number of scaffolds	85
N50	30,600,000 bp
Predicted transcripts	41,742
Annotated genes	30,097
Assembly BUSCO score (embryophyta_odb10)	98.2%
Annotation BUSCO score (embryophyta_odb10)	97.1%

Assembly

The Citrus sinensis cv. Neixiu genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file)

C.sinensis_Neixiu_v1.0.a1.fasta.gz

Gene Predictions

The Citrus sinensis cv. Neixiu v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file)	C.sinensis_Neixiu_v1.0.a1.genes.gff3.gz
Protein sequences (FASTA file)	C.sinensis_Neixiu_v1.0.a1.protein.fasta.gz
Transcript sequences (FASTA file)	C.sinensis_Neixiu_v1.0.a1.Transcript.fasta.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus sinensis cv. Neixiu genome v1.0 are available for download below. The Citrus sinensis genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan	Csinensis_Neixiu_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Csinensis_Neixiu_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Csinensis_Neixiu_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Csinensis_Neixiu_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus sinensis cv. Neixiu genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e^-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format.

Protein Homologs

C. sinensis cv. Neixiu v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cs_Neixiu_v1.0_vs_arabidopsis.xlsx.gz
C. sinensis cv. Neixiu v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cs_Neixiu_v1.0_vs_arabidopsis_hit.fasta.gz
C. sinensis cv. Neixiu v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cs_Neixiu_v1.0_vs_arabidopsis_noHit.fasta.gz
C. sinensis cv. Neixiu v1.0 proteins with SwissProt homologs (EXCEL file)	Cs_Neixiu_v1.0_vs_swissprot.xlsx.gz
C. sinensis cv. Neixiu v1.0 proteins with SwissProt (FASTA file)	Cs_Neixiu_v1.0_vs_swissprot_hit.fasta.gz
C. sinensis cv. Neixiu v1.0 proteins without SwissProt (FASTA file)	Cs_Neixiu_v1.0_vs_swissprot_noHit.fasta.gz
C. sinensis cv. Neixiu v1.0 proteins with TrEMBL homologs (EXCEL file)	Cs_Neixiu_v1.0_vs_trembl.xlsx.gz
C. sinensis cv. Neixiu v1.0 proteins with TrEMBL (FASTA file)	Cs_Neixiu_v1.0_vs_trembl_hit.fasta.gz
C. sinensis cv. Neixiu v1.0 proteins without TrEMBL (FASTA file)	Cs_Neixiu_v1.0_vs_trembl_noHit.fasta.gz